Too many generalizations in this thread. "An OTA" means many things. Some are at least and others are fly-by-night. The bottom line is that if you can save money and nothing goes wrong with your trip, it really doesn't matter so long as the OTA issues your e-ticket in the first place.
Before you use an OTA, do your research to make sure that it is not fly-by-night. The shoddy ones will have plenty of negative reviews.
Before you use an OTA, understand its T&C's which are in addition to whatever the air carrier sets.
Before you use an OTA, make certain that you understand the fare rules of the ticket(s) you are purchasing. In all too many situations, the savings are achieved because you are being sold a consolidator fare or multiple tickets rather than a connection. Nothing wrong with either of those, but you need to know that in the first instance, it may be wholly inflexible and in the latter, you may have no protection if you are late in arriving on your first flight.
One loused up trick can cost a lot of PSL's and the least expensive ticket is not always the least expensive trip. You might ask yourself why a reputable bricks and mortar TA charges you a fee and why, if you are busy or inexperienced, it may be well worth that fee.
But, if you need to make a change or there are IRROPS, that is where the differences arise.